That's truly odd. The error happens when the offending file is imported, which
it is a syntax issue that should have been seen earlier. I'll take a look at
this soon (unless someone
else beats me to it).
In the meantime, of course, do not use the use_tasked_jobs on this instance of
Galaxy. If others
have seen similar issues, then please speak up.
----- Original Message -----
> I am using Python 2.7. I am running with an hg checked out, up to
> date version of " https://bitbucket.org/galaxy/galaxy-dist/ ".
> I am very new to Galaxy. I have an instance setup and running
> locally. I am able to perform routine actions such as uploading
> files, processing with Picard, and aligning with BWA. I have been
> able to make the jobs execute out our SGE cluster.
> In order to better utilize my cluster, I attempted to enable
> parallelism of the tasks that support it (such as BWA) by
> configuring the universe_wsgi.ini file with the parameter
> use_tasked_jobs = True
> When I do this and attempt execute a BWA alignment on a 4.1Gb fastq
> file, I am given the error
> > Result 256 from mv
> > /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/job_working_directory/000/21/task_1/dataset_21.dat
> > /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/files/000/dataset_21.dat
> > /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/job_working_directory/000/21/task_0:
> > Traceback (most recent call last):
> > File "./scripts/extract_dataset_part.py", line 25, in ?
> > import galaxy.model.mapping #need to load this before we unpickle,
> > in
> > order to setup properties assigned by the mappers
> > File
> > "/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/lib/galaxy/model/__init__.py",
> > line 13, in ?
> > import galaxy.datatypes.registry
> > File
> > "/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/lib/galaxy/datatypes/registry.py",
> > line 146
> > finally:
> > ^
> > SyntaxError: invalid syntax
> > The alignment failed.
> If you need the complete error message, contact me and I can supply
> you with it. It's too large to paste in-line and attachments aren't
> Is there more I need to do to enable parallel jobs (splitting of
> input, align, then merge)?
> Any suggestions are greatly appreciated.
> The Galaxy User list should be used for the discussion of
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> use the Galaxy Development list:
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> please use the interface at:
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at: